Doc-Alignment

  Inter-genomic and intra-genomic comparisons can help reveal the structural complexity of Cucurbitales genomes. We used V.vinifera as a reference, and by comparing homologous gene locus maps and Ks values between V.vinifera and other Cucurbitales, we could separate orthologous and paralogous genes produced by different polyploidization in the species genomes. We created a hierarchical lists of homologous genes using V.vinifera as a reference.
  The relevant gene ids can be obtained from the Cucurbitales blast and match under the Tools module. This link is Cucurbitales blast and match.

Orthogroup analysis platform
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Select Vvi1 Blo1 Blo2 Bda1 Bda2 Bpe1 Bpe2 Bma1 Bma2 Cmo1 Cmo2 Cma1 Cma2 Car1 Car2 Sed1 Cpe1 Cpe2 Bhi1 Tan1 Cmetu1 Lac1 Hepe1 Mch1 Lcy1 Cla1 Cam1 Cec1 Cco1 Clacu1 Cmu1 Cre1 Cone1 Cone2 Cone3 Cone4 Lsi1 Csa1 Chy1 Cme1 Blo3 Blo4 Bda3 Bda4 Bpe3 Bpe4 Bma3 Bma4 Sed2 Cmo3 Cmo4 Cma3 Cma4 Car3 Car4 Cpe3 Cpe4 Bhi2 Tan2 Cmetu2 Lac2 Hepe2 Mch2 Lcy2 Cla2 Cam2 Cec2 Cco2 Clacu2 Cmu2 Cre2 Lsi2 Csa2 Chy2 Cme2
Vvi2g612 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g613 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bhi05g00527 . . . . . . . . . . . . . . . . .
Vvi2g614 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone14ag1105 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g615 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g616 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g617 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g618 . . . . . . . . . . Cma02g01585 . Car02g01349 . . . . . . . . . . . . . . . . . . Cone8ag0448 Cone12ag0437 . . . . Chy04g00049 . . . . . . . . . . Cmo02g01628 . . . . . . . . . . . . . . Cla09g01177 Cam09g1242 Cec09g1258 . . . Cre09g1206 . Csa03g04651 . Cme04g00063
Vvi2g619 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g620 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g621 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone12ag0438 . . . . Chy04g00050 . . . . . . . Bma05g00717 . . . Cmo19g00502 . . . . . . Bhi05g00520 . . . . . . Cla09g01176 Cam09g1241 Cec09g1257 Cco09g1287 . . Cre09g1205 . Csa03g04650 . Cme04g00064
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
5 12320971 12329257 + XM_039031626.1 Bhi05g00520 520
5 12424369 12427759 + XM_039031785.1 Bhi05g00527 527
5 41456862 41461971 - Bma021795.1 Bma05g00717 717
9 14210435 14217310 - CaPI482276_09g012410.1 Cam09g1241 1241
9 14227647 14232485 - CaPI482276_09g012420.1 Cam09g1242 1242
2 8929864 8934517 + Carg08816-RA Car02g01349 1349
9 14106067 14112939 - CcPI632755_09g012870.1 Cco09g1287 1287
9 14237791 14244645 - CePI673135_09g012570.1 Cec09g1257 1257
9 14266343 14271223 - CePI673135_09g012580.1 Cec09g1258 1258
4 547440 551529 + Chy4G067670.1 Chy04g00049 49
4 554888 561523 + Chy4G067680.1 Chy04g00050 50
9 14179931 14187926 - ClCG09G012390.1 Cla09g01176 1176
9 14197935 14203237 - ClCG09G012400.1 Cla09g01177 1177
2 9016191 9022540 + CmaCh02G015850.1 Cma02g01585 1585
4 480041 485466 + MELO3C003369.2.1 Cme04g00063 63
4 487513 496783 + MELO3C003370.2.1 Cme04g00064 64
2 9394192 9398413 + CmoCh02G016280.1 Cmo02g01628 1628
19 5964509 5981207 - CmoCh19G005020.1 Cmo19g00502 502
8 2851468 2855435 + Conep08aG0046500.1 Cone8ag0448 448
12 2604368 2609153 + Conep12aG0045200.1 Cone12ag0437 437
12 2609726 2614978 + Conep12aG0045300.1 Cone12ag0438 438
14 9216684 9217353 + Conep14aG0112700.1 Cone14ag1105 1105
9 14278578 14285773 - CrPI670011_09g012050.1 Cre09g1205 1205
9 14299465 14304262 - CrPI670011_09g012060.1 Cre09g1206 1206
3 40390066 40399730 - CsaV3_3G049560.1 Csa03g04650 4650
3 40402128 40406681 - CsaV3_3G049570.1 Csa03g04651 4651
2 6513126 6524677 + Vvi2g612 Vvi2g612 612
2 6526980 6534000 - Vvi2g613 Vvi2g613 613
2 6548154 6549076 - Vvi2g614 Vvi2g614 614
2 6558534 6560391 + Vvi2g615 Vvi2g615 615
2 6570700 6570874 + Vvi2g616 Vvi2g616 616
2 6597030 6597204 + Vvi2g617 Vvi2g617 617
2 6621101 6629838 + Vvi2g618 Vvi2g618 618
2 6634761 6636649 + Vvi2g619 Vvi2g619 619
2 6637767 6638812 - Vvi2g620 Vvi2g620 620
2 6646931 6657662 + Vvi2g621 Vvi2g621 621
       

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